Secondary protein structures alternative conformations

NMR and kinetic studies have been conducted with the hope of providing more details about the position and conformation of the polypeptide substrate in cAMP-dependent protein kinase. These have served to narrow down the possible spatial relationships between enzyme bound ATP and the phosphorylated serine. Thus, a picture of the active site that is consistent with the available data can be drawn (12,13,66,67). Although these studies have been largely successful at eliminating some classes of secondary polypeptide structure such as oi-hellces, 6-sheets or an obligatory 6-turn conformation 66), the precise conformation of the substrate is still not known. The data are consistent with a preference for certain 6-turn structures directly Involving the phosphorylated serine residue. However, they are also consistent with a preference or requirement for either a coil structure or some nonspecific type of secondary structure. Models of the ternary active-site complexes based on both the coil and the, turn conformations of one alternate peptide substrate have" been constructed (12). These two models are consistent with the available kinetic and NMR data. 

When secondary chemical equilibrium prevail, such as salt in or salt out effects involving changes in the self-association or aggregation state of the polypeptide or protein, or alternatively when additional hydrophobic interaction effects are manifested, or finally if conformational transitions are induced due to the choice of a water structuring or water-destabilizing salt species from the Hofmeister series,91-93 then divergences from this ideal behavior will be evident. 

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

Most of the above membrane-oriented studies were carried out for peptides in multilayer systems that were collapsed or transferred onto a sample cell surface. An alternative and very interesting way to study membrane systems is by IRRAS (infrared reflection absorption spectroscopy) at the air-water interface. In this way, unilamellar systems can be studied as a function of surface pressure and under the influence of various membrane proteins and peptides added. Mendelsohn et al.[136] have studied a model series of peptides, [K2(LA) ] (n = 6, 8, 10, 12), in nonaqueous (solution), multilamellar (lipid), and unilamellar (peptide-IRRAS) conditions. In the multilamellar vesicles these peptides are predominantly helical in conformation, but as peptide only monolayers on a D20 subphase the conformation is (1-sheet like, at least initially. For different lengths, the peptides show variable surface pressure sensitivity to development of some helical component. These authors further use their IR data to hypothesize the existence of the less-usual parallel (i-sheet conformation in these peptides. A critical comparison is available for different secondary structures as detected using the IRRAS data for peptides on H20 and D20 subphasesJ137 ... 

Alternatively, a protein might have a pleated sheet conformation, more common with sequences of amino acid units with small R groups on the a-carbon (see Figure 3-lb). Thus, the secondary structure for a given protein depends in large part upon the tendency of the R groups to attract or repel each other along the chain. In other words, the secondary structure is dependent upon the primary structure. 

Other IRRAS applications to peptides and proteins. In addition to the pulmonary surfactant system, a variety of other applications employing IRRAS to study peptide and protein conformation and orientation have appeared. The secondary structure conversion of the amyloid (prion)-protein in the normal form into the abnormal form is the main cause of several human and animal diseases, such as Alzheimer s disease [68]. The secondary structure of the first 40 residues of the amyloid protein was detected by circular dichroism (CD) in aqueous solution and with IRRAS at the interface. A stable /1-sheet-enriched state of the amyloid is formed at the air-water interface, in contrast to the initial bulk solution containing high a-helix/random coil and low /l-sheet parts. The change in the pH going from bulk (alkaline pH) to the interface (neutral or slightly acidic pH) can have effects on the conformation at the interface. Another alternative might be the intrinsic hydrophobicity of the air-water interface, which is a hydrophobic-hydrophilic system with air as the hydrophobic part. 

For this purpose, it has been demonstrated that the high resolution solid-state NMR approach provides one with an alternative and convenient means to distinguish a variety of crystalline polymorphs and to reveal the secondary structures of biological macromolecules, because the chemical shifts of backbone carbons are displaced (up to 8 ppm) [1, 2] depending on their respective conformations. In addition, it is emphasized that this type of empirical approach can be used as a very valuable constraint to construct the three-dimensional structure of biological molecules, such as peptides and proteins, based on a set of accurately determined interatomic distances measured by a partial dipolar recoupling method, such as REDOR (rotational echo double resonance) [3-6]. 

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